Changes between Version 51 and Version 52 of se.lu.onk.IlluminaSNPNormalization


Ignore:
Timestamp:
Mar 13, 2009, 6:31:44 PM (12 years ago)
Author:
markus
Comment:

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  • se.lu.onk.IlluminaSNPNormalization

    v51 v52  
    1010
    1111=== News ===
     12
     13 * Mar. 13, 2009. tQN 1.1.2 released. This is a minor bug-fix release. 'split_samples.pl' has been modified to replace commas (,) with points(.) in data columns as !BeadStudio exports data with commas for some language settings, which caused problems for tQN.
     14
    1215
    1316 * Jan. 15, 2009. tQN 1.1.1 released. This is a minor bug-fix release to handle not only NaN but also NA for missing values in files from !BeadStudio. !BeadStudio only outputs NaN but reformatting in for example Excel may change NaN to NA, which previously resulted in erroneous results from tQN.
     
    2932=== Download tQN ===
    3033
    31 [http://cbbp.thep.lu.se/~markus/software/tQN/tQN-1.1.1.zip?format=raw Download the latest stand-alone release (tQN-1.1.1)]. This release includes tQN cluster files for humanhap300, humanhap300-duo, humancnv370-duo, humancvn370-quad, humanhap550, human610-quad, and human1M-duo.
     34[http://cbbp.thep.lu.se/~markus/software/tQN/tQN-1.1.2.zip?format=raw Download the latest stand-alone release (tQN-1.1.2)]. This release includes tQN cluster files for humanhap300, humanhap300-duo, humancnv370-duo, humancvn370-quad, humanhap550, human610-quad, and human1M-duo.
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    7376    perl split_samples.pl --data_file=example/example_beadstudio_data.txt
    7477  }}}
    75   where ''example_beadstudio_data.txt'' is a file exported from !BeadStudio in the format described above.
     78  where ''example_beadstudio_data.txt'' is a file exported from !BeadStudio in the format described above. With some language settings !BeadStudio exports files with commas (,) as decimal points; 'split_samples.pl' replaces all commas (,) in data columns with points (.) in the 'split_samples.pl' results files.
    7679
    7780  This script will generate one file per sample together with a file ''sample_names.txt'' in the tQN subdirectory ''extracted''. These files are used when tQN is run and can be deleted once the samples are normalized.
     
    8588  }}}
    8689
    87   This command will perform tQN on the samples in the tQN subdirectory ''extracted'' that are specified in the file ''sample_names.txt''. If you want to perform tQN on a subset of samples you can edit ''sample_names.txt'' accordingly. The normalized data is stored in the tQN subdirectory ''normalized''. For each sample, there is a file with tQN normalized data. A file ''tQN_beadstudio.txt'' is also generated with tQN B allele frequencies and Log R ratios for all samples in a format suitable for import into !BeadStudio using its import sub-column process. tQN also supports generating tQN data for further analysis with PennCNV, QuantiSNP and BAFsegmentation. Running tQN with the following command:
     90  This command will perform tQN on the samples in the tQN subdirectory ''extracted'' that are specified in the file ''sample_names.txt''. If you want to perform tQN on a subset of samples you can edit ''sample_names.txt'' accordingly. tQN requires that points (.) are used as decimal points. The normalized data is stored in the tQN subdirectory ''normalized''. For each sample, there is a file with tQN normalized data. A file ''tQN_beadstudio.txt'' is also generated with tQN B allele frequencies and Log R ratios for all samples in a format suitable for import into !BeadStudio using its import sub-column process. tQN also supports generating tQN data for further analysis with PennCNV, QuantiSNP and BAFsegmentation. Running tQN with the following command:
    8891
    8992  {{{